藏东南典型暗针叶林不同土壤剖面微生物群落特征

深层土壤中的微生物群落对陆地生态系统养分和能量循环转化过程不可或缺,研究青藏高原典型暗针叶林带土壤微生物群落在土壤垂直剖面的变化特征,对深入认识高寒区域森林生态系统土壤微生物群落构建特征及全球变化影响预测具有重要意义。运用Illumina Miseq高通量测序技术和分子生态网络分析,研究藏东南色季拉山暗针叶林带表层（0-20 cm）和底层土壤（40-60 cm）微生物群落组成及分子生态网络结构。研究结果表明随着土壤深度增加,真菌和细菌的丰富度和Shannon多样性指数显著降低。主坐标分析（PCoA）显示土壤深度显著影响真菌和细菌的群落结构（P < 0.01）。不同微生物种群对土壤深度的响应有显著差异,座囊菌纲（Dothideomycetes）、银耳纲（Tremellomycetes）和拟杆菌门（Bacteroidetes）、变形菌门（Proteobacteria）的相对丰度随剖面加深而显著降低,而古菌根菌纲（Archaeorhizomycetes）和绿弯菌门（Chloroflexi）则显著增加。分子生态网络分析发现,真菌网络以负相关连接为主（占总连接数65%-98%）,而细菌网络以正相关连接为主（69%-75%）,真菌和细菌网络中正相关连接的比例均随剖面加深而增加。底层土壤真菌和细菌网络的平均连接度和平均聚类系数均高于表层土壤,说明微生物网络随土壤深度的增加而变得更复杂。真菌网络的平均路径距离和模块性在底层土壤均大于表层土壤,意味着真菌网络应对环境变化的稳定性随剖面加深而增加,而细菌网络则正相反,在表层土壤的稳定性更强。真菌网络中连接节点的个数随剖面加深而增加,锤舌菌纲（Leotiomycetes）是连接网络模块的关键菌种;在细菌网络中模块枢纽和连接节点则随剖面加深而降低,并且放线菌门、变形菌门等关键种群在分子生态网络中的功能在表层和底层土壤有明显差异。综上所述,藏东南色季拉山暗针叶林带深层土壤中微生物群落特征与表层土壤有显著差别,揭示影响深层土壤微生物网络构建和稳定的关键种群,对深入理解和预测青藏高原森林生态系统对全球变化的响应与反馈有重要意义。     

Effects of cotton–maize rotation on soil microbiome structure

Verticillium wilt is a disastrous disease in cotton-growing regions in China. As a common management method, cotton rotation with cereal crops is used to minimize the loss caused by Verticillium dahliae. However, the correlation between soil microbiome and the control of Verticillium wilt under a crop rotation system is unclear. Therefore, three cropping systems (fallow, cotton continuous cropping, and cotton–maize rotation) were designed and applied for three generations under greenhouse conditions to investigate the different responses of the soil microbial community. The soil used in this study was taken from a long-term cotton continuous cropping field and inoculated with V. dahliae before use. Our results showed that the diversity of the soil bacterial community was increased under cotton–maize rotation, while the diversity of the fungal community was obviously decreased. Meanwhile, the structure and composition of the bacterial communities were similar even under the different cropping systems, but they differed in the soil fungal communities. Through microbial network interaction analysis, we found that Verticillium interacted with 17 bacterial genera, among which Terrabacter had the highest correlation with Verticillium. Furthermore, eight fungal and eight bacterial species were significantly correlated with V. dahliae. Collectively, this work aimed to study the interactions among V. dahliae, the soil microbiome, and plant hosts, and elucidate the relationship between crop rotation and soil microbiome, providing a new theoretical basis to screen the biological agents that may contribute to Verticillium wilt control.     

Vertical distribution of fungal communities in tallgrass prairie soil

We used 454 sequencing of the internal transcribed spacer region to characterize fungal communities in tallgrass prairie soils subdivided into strata 0-10, 10-20, 30-40 and 50-60 cm deep. The dataset included more than 14000 fungal sequences distributed across Basidiomycota, Ascomycota, basal fungal lineages and Glomeromycota in order of decreasing frequency. As expected the community richness and diversity estimators tended to decrease with increasing depth. Although species richness was significantly reduced for samples from the deeper profiles, even the deepest stratum sampled contained richness of more than a third of that in the topmost stratum. More importantly, nonparametric multidimensional scaling (NMS) ordination analyses indicated that the fungal communities differed across vertical profiles, although only the topmost and deepest strata were significantly different when the NMS axis scores were compared by ANOVA. These results emphasize the importance of considering the fungal communities across the vertical strata because the deeper soil horizons might maintain a distinct community composition and thus contribute greatly to overall richness. The majority of operational taxonomic units (OTUs) declined in frequency with increasing depth, although a linear regression analysis indicated that some increased with increasing depth. The OTUs and BLAST-assigned taxa that showed increasing frequencies were mainly unculturable fungi, but some showed likely affinities to families Nectriaceae and Venturiaceae or to genus Pachnocybe. Although the ecological roles of the fungi in the deeper strata remain uncertain, we hypothesize that the fungi with preferences for deeper soil have adequate access to substrates and possess environmental tolerances that enable their persistence in those environments.     

城乡不同绿地中毛白杨土壤及根系真菌群落结构研究

土壤微生物在土壤养分循环和能量流动等生物过程中起着重要的作用,并且能敏感地响应环境条件的变化。本研究以天津市宝坻区毛白杨Populus tomentosa为研究对象,探究3种不同环境条件(社区绿地CG、公园绿地PG和高速公路旁绿地HG)对毛白杨土壤和根系真菌群落结构的影响。研究结果表明,3个绿地间土壤真菌Shannon多样性指数存在显著差异(HG>CG>PG);但根系真菌Shannon多样性指数无显著差异;此外,不同环境条件对真菌群落的组成起着重要作用。毛白杨土壤和根系真菌群落组成主要为丝盖伞属Inocybe、地孔块菌属Geopora、被孢霉属Mortierella、棉革菌属Tomentella、蓝状菌属Talaromyces、块菌属Tuber、层腹菌属Hymenogaster、链格孢属Alternaria、革菌属Thelephora、克努夫菌属Knufia和桩菇菌属Paxillus等,且差异分析表明丝盖伞属Inocybe、棉革菌属Tomentella和地孔块菌属Geopora的相对多度在3个样地中差异显著。比较分析土壤和根系样品发现土壤真菌群落α多样性显著高于根系真菌群落,两部位的真菌群落结构存在显著差异,块菌属Tuber的相对多度在根系样品中显著高于土壤样品。真菌群落功能预测表明腐生功能类群在不同环境条件下和不同部位间均存在显著差异。研究结果阐述了环境变化对土壤微生物群落中真菌组的影响,为森林生态系统的保护和林地可持续发展提供重要理论依据。     

Evolution of bacterial communities in the wheat crop rhizosphere

The gap between current average global wheat yields and that achievable through best agronomic management and crop genetics is large. This is notable in intensive wheat rotations which are widely used. Expectations are that this gap can be reduced by manipulating soil processes, especially those that involve microbial ecology. Cross‐year analysis of the soil microbiome in an intensive wheat cropping system revealed that rhizosphere bacteria changed much more than the bulk soil community. Dominant factors influencing populations included binding to roots, plant age, site and planting sequence. We demonstrated evolution of bacterial communities within the field rhizosphere. Early in the season, communities tightly bound to the root were simplest. These increased in diversity with plant age and senescence. Loosely bound communities also increased in diversity from vegetative to reproductive plant stages but were more stable than those tightly bound to roots. Planting sequence and, to a lesser extent, wheat genotype also significantly affected rhizosphere bacteria. Plasticity in the rhizosphere generated from crop root system management and genetics offers promise for manipulating the soil ecology of intense cereal systems. Analyses of soil microbiomes for the purpose of developing agronomic benefit should include roots as well as soil loosely adhered to the roots, and the bulk soil.     

Fungal community diversity and soil health in intensive potato cropping systems of the east Po valley, northern Italy

An ecological approach was used to investigate the relationship between diversity of soil fungal communities and soil‐borne pathogen inoculum in a potato growing area of northern Italy affected by yield decline. The study was performed in 14 sites with the same tillage management practices: 10 named ‘potato sites’, that for many years had been intensely cultivated with potatoes, and 4 named ‘rotation sites’, subject to a 4‐year rotation without potatoes or any recurrent crop for many years. Fungal communities were recorded using conventional (soil fungi by plate count and endophytic fungi as infection frequency on pot‐grown potato plant roots in soil samples) and molecular approaches [Basidiomycetes and Ascomycetes with specific and denaturing gradient gel electrophoresis (DGGE) analysis]. Diversity of fungal communities in potato sites was significantly lower than that in rotation sites. In addition, fungal communities in rotation sites showed lower Berger–Parker dominance than those in the potato sites, suggesting that rotation sites had a higher diversity as well as a better fungal community balance than potato sites. The ANalysis Of SIMilarity test of soil fungi and root endophytic fungi revealed that the two cropping systems differed significantly for species composition. Root endophytic fungal communities showed a greater ability to colonise potato roots in soil samples from potato sites than those from rotation sites. Moreover, the majority of endophytic root fungal community species in potato sites belonged to the potato root rot complex and storage disease (Colletotrichum coccodes, Fusarium solani and Fusarium oxysporum), while those in rotation sites were mainly ubiquitous or saprobic fungi. Soil rDNA analyses showed that Ascomycetes were much more frequent than Basidiomycetes in all the soils examined. DGGE analysis, with the Ascomycete‐specific primer (ITS1F/ITS4A), did not reveal distinctions between the communities found at the potato and rotation sites, although the same analysis showed differences between the communities of Basidiomycetes (specific primer ITS1F/ITS4B). These findings showed that recurrent potato cropping affected diversity and composition of soil fungal communities and induced a shift in specialisation of the endophytic fungi towards potato.     

Differential sensitivity of total and active soil microbial communities to drought and forest management

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning—that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 60 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community‐based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought‐plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change.     

Growth response of crops to soil microbial communities from conventional monocropping and tree-based intercropping systems

Background and aims

Recent studies have shown that tree-based intercropping (TBI) systems support a more diverse soil microbial community compared to conventional agricultural systems. However, it is unclear whether differences in soil microbial diversity between these two agricultural systems have a functional effect on crop growth.

Methods

In this study, we used a series of greenhouse experiments to test whether crops respond differently to the total soil microbial community (Experiment 1) and to arbuscular mycorrhizal (AM) fungal communities alone (Experiment 2) from conventionally monocropped (CM) and TBI systems.

Results

The crops had a similar growth response to the total soil microbial communities from both cropping systems. However, when compared to sterilized controls, barley (Hordeum vulgare) and canola (Brassica napus) exhibited a negative growth response to the total soil microbial communities, while soybean (Glycine max) was unaffected. During the AM fungal establishment phase of the second experiment, ‘nurse’ plants had a strong positive growth response to AM fungal inoculation, and significantly higher biomass when inoculated with AM fungi from the CM system compared to the TBI system. Soybean was the only crop species to exhibit a significant positive growth response to AM fungal inoculation. Similar to the total soil microbial communities, AM fungi from the two cropping systems did not differ in their effect on crop growth.

Conclusion

Overall, AM fungi from both cropping systems had a positive effect on the growth of plants that formed a functional symbiosis. However, the results from these experiments suggest that negative effects of non-AM fungal microbes are stronger than the beneficial effects of AM fungi from these cropping systems.     

Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils

Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.     

Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root

While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities.     

利用DGGE法研究不同种植体系中根际微生物群落结构

利用DGGE技术研究不同间作和轮作种植体系对作物根际细菌和真菌群落结构的影响.运用16SrDNA和18SrDNA特异引物对,将土壤中提取的总DNA进行PCR扩增后,通过DGGE技术对PCR产物进行分析,结果表明:玉米-蚕豆轮作对蚕豆根际细菌和真菌群落结构影响明显,二者都与单作蚕豆有较大差异;小麦/蚕豆间作明显改变两种作物根际细菌群落结构和蚕豆根际真菌群落结构;玉米/蚕豆间作明显改变玉米根际细菌、真菌群落结构和蚕豆根际真菌群落结构.     

小麦根系分泌物对黄瓜生长及土壤真菌群落结构的影响

以黄瓜为受体,以不同化感效应(促进/抑制)小麦品种为供体,采用PCR-DGGE技术,研究了小麦根系分泌物及伴生小麦对黄瓜生长及土壤真菌群落结构的影响.结果表明： 在处理第6天和第12天,化感促进效应小麦根系分泌物分别显著提高了黄瓜幼苗株高和茎粗;在处理第18天,化感促进和抑制效应小麦根系分泌物均显著提高了黄瓜幼苗株高;在处理第6天,不同化感效应小麦根系分泌物均显著降低了黄瓜幼苗根际土壤真菌群落条带数、Shannon指数及均匀度指数,有苗对照(W)显著高于无苗对照(Wn);在处理第18天,各处理的真菌群落结构条带数、Shannon指数及均匀度指数均显著高于无苗对照(Wn).伴生化感抑制效应小麦显著降低了黄瓜根际土壤真菌群落Shannon指数和均匀度指数,说明小麦根系分泌物及伴生小麦改变了土壤真菌群落结构.DGGE图谱及其主成分分析结果表明,伴生不同化感效应小麦对土壤真菌群落结构影响较大.     

Specificity of root microbiomes in native‐grown Nicotiana attenuata and plant responses to UVB increase Deinococcus colonization

Plants recruit microbial communities from the soil in which they germinate. Our understanding of the recruitment process and the factors affecting it is still limited for most microbial taxa. We analysed several factors potentially affecting root microbiome structure – the importance of geographic location of natural populations, the microbiome of native seeds as putative source of colonization and the effect of a plant's response to UVB exposure on root colonization of highly abundant species. The microbiome of Nicotiana attenuata seeds was determined by a culture‐dependent and culture‐independent approach, and the root microbiome of natural N. attenuata populations from five different locations was analysed using 454‐pyrosequencing. To specifically address the influence of UVB light on root colonization by Deinococcus, a genus abundant and consistently present in N. attenuata roots, transgenic lines impaired in UVB perception (irUVR8) and response (irCHAL) were investigated in a microcosm experiment with/without UVB supplementation using a synthetic bacterial community. The seed microbiome analysis indicated that N. attenuata seeds are sterile. Alpha and beta diversities of native root bacterial communities differed significantly between soil and root, while location had only a significant effect on the fungal but not the bacterial root communities. With UVB supplementation, root colonization of Deinococcus increased in wild type, but decreased in irUVR8 and irCHAL plants compared to nontreated plants. Our results suggest that N. attenuata recruits a core root microbiome exclusively from soil, with fungal root colonization being less selective than bacterial colonization. Root colonization by Deinococcus depends on the plant's response to UVB.     

秦岭火地塘真菌群落海拔分布格局

土壤真菌在自然生态系统的养分循环和土壤碳储存方面起重要作用。秦岭火地塘林区在不同海拔分布着不同的优势树种,但其相应的土壤特征及微生物群落的海拔分布格局仍不明晰。本研究分析了5个海拔处(1500、1700、1900、2100和2300 m)的土壤特征变化趋势,并在高通量测序基础上研究了真菌群落格局。结果表明: 土壤有效磷含量、pH值随海拔的增加而显著增加,土壤水分则呈下降趋势。土壤真菌Shannon多样性指数随海拔升高呈下降趋势,而ACE丰度指数相反;真菌优势门为担子菌门(68.2%)、子囊菌门(19.8%)和球囊菌门(1.7%),且随海拔升高整体呈现出“U”型或“单峰”变化格局;真菌优势纲为伞菌纲(64.2%)、粪壳菌纲(5.8%)和锤舌菌纲(4.1%)。冗余分析(RDA)表明,土壤特性解释了土壤真菌群落总变异的89.1%,其中土壤有效磷含量、pH和海拔是土壤真菌群落海拔梯度变化的主要驱动因子。在秦岭火地塘林区,土壤特征在海拔梯度上的差异性影响了土壤真菌群落组成。     

植茶年限对土壤微生物群落结构及多样性的影响

为探明植茶年限对土壤微生物群落结构及多样性的影响,以0、20、25、38和48年茶园土壤表层(0～20 cm)、亚表层(20～40 cm)土壤样品为研究对象,采用T-RFLP技术及qPCR方法对土壤细菌(B)、真菌(F)群落进行分析。结果表明: 植茶后土壤理化性质明显改变,随植茶年限的增加土壤有机碳、碱解氮及有效磷含量呈先升高后降低的趋势,表层土壤有机碳和全氮含量均显著高于亚表层土壤。不同植茶年限土壤细菌群落组分存在差异且多样性指数随植茶年限的增加呈下降趋势,而不同植茶年限土壤真菌群落组分差异不明显且多样性指数无显著差异。总体来看,土壤细菌群落对植茶年限的响应比真菌群落敏感。随植茶年限的增加,茶园土壤微生物群落有从F/B较低的“细菌型”向F/B较高的“真菌型”转变的趋势。     

The root microbiome: Community assembly and its contributions to plant fitness

The root microbiome refers to the community of microbes living in association with a plant's roots, and includes mutualists, pathogens, and commensals. Here we focus on recent advances in the study of root commensal community which is the major research object of microbiome-related researches. With the rapid development of new technologies, plant–commensal interactions can be explored with unprecedented breadth and depth. Both the soil environment and the host plant drive commensal community assembly. The bulk soil is the seed bank of potential commensals, and plants use root exudates and immune responses to build healthy microbial communities from the available microbes. The plant microbiome extends the functional system of plants by participating in a variety of processes, including nutrient absorption, growth promotion, and resistance to biotic and abiotic stresses. Plants and their microbiomes have evolved adaptation strategies over time. However, there is still a huge gap in our understanding of the regulatory mechanisms of plant–commensal interactions. In this review, we summarize recent research on the assembly of root microbial communities and the effects of these communities on plant growth and development, and look at the prospects for promoting sustainable agricultural development through the study of the root microbiome.     

Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field‐based tree experiment

Exploring the link between above‐ and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well‐recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field‐based tree experiment in Minnesota, USA, to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). The phylum effect was caused by differences in ectomycorrhizal fungal community composition, while the origin effect was attributable to differences in community heterogeneity. Taken together, this study emphasizes that plant‐associated effects on soil fungal communities are largely guild‐specific and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness.     

添加高粱根茬根际土对连作黄瓜生长和根际微生物的影响

为了分析添加高粱根茬根际土对连作黄瓜生长和根际微生物群落特征的影响,本研究通过盆栽试验,采用荧光定量PCR和高通量测序技术分析土壤细菌和真菌群落组成的差异。试验共设4个处理: CK(不施肥),T₁(单施化肥),T₂(优化施肥),T₃(优化施肥+高粱根茬根际土)。结果表明: 与其他处理相比,T₃处理促进了黄瓜生长发育,提高了土壤中16S rRNA和ITS rRNA基因数量。与T₁处理相比,T₂和T₃处理明显提高了细菌群落的丰富度和多样性,不同处理间真菌群落的丰富度和多样性差异不明显。添加高粱根茬根际土在一定程度上改变了基于门、属水平上的细菌和真菌群落结构。其中,细菌中提高了酸杆菌门和拟杆菌门的丰度,降低了变形菌门、厚壁菌门、硝化螺旋菌门和芽孢杆菌属的丰度;真菌中提高了担子菌门、木霉菌属和假散囊菌属的丰度,降低了镰刀菌属和绿僵菌属的丰度。冗余分析表明,土壤硝态氮和有机质含量分别是影响细菌和真菌群落结构差异的关键因子。添加高粱根茬根际土不仅提高了连作黄瓜土壤微生物数量和细菌多样性,而且增加了有益菌木霉菌属的丰度,降低了致病镰刀菌的丰度和数量,保障了黄瓜存活率,为缓解黄瓜连作障碍提供了一条切实可行的解决途径。     

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Microbial communities in plant roots provide critical links between above‐ and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities, we designed a trap‐plant bioassay experiment. Replicate Populus, Quercus and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of four loci (i.e., 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.